8dga: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[8dga]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DGA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DGA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.73&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8dga FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dga OCA], [https://pdbe.org/8dga PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dga RCSB], [https://www.ebi.ac.uk/pdbsum/8dga PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dga ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/DCR1_DROME DCR1_DROME] Essential for RNA interference (RNAi); double-stranded RNA (dsRNA) induces potent and specific gene silencing. RNAi is mediated by the RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys or silences messenger RNAs homologous to the silencing trigger. May carry out the initiation step of RNAi by cleaving dsRNA to produce 22 bp dsRNAs (siRNAs) which target the selective destruction of homologous RNAs. During embryogenesis, involved in germline fate determination.<ref>PMID:11201747</ref> <ref>PMID:11498593</ref> <ref>PMID:16949822</ref>
+[https://www.uniprot.org/uniprot/DCR1_DROME DCR1_DROME] Endoribonuclease which functions in microRNA- (miRNA) gene silencing and, independently of its ribonuclease III activity, also acts in the short interfering RNA- (siRNA) gene silencing pathway (PubMed:11201747, PubMed:11498593, PubMed:15066283, PubMed:15918769, PubMed:15985611, PubMed:17666393, PubMed:17928574, PubMed:19451544, PubMed:19635780, PubMed:21419681, PubMed:21926993, PubMed:24488111, PubMed:36182693). Cleaves hairpin precursor miRNAs (pre-miRNA) to generate mature miRNAs (miRNAs) that are between twenty-one to twenty-four nucleotides in length and function in RNA silencing and post-transcriptional regulation of gene expression (PubMed:15066283, PubMed:15918769, PubMed:15985611, PubMed:17666393, PubMed:17928574, PubMed:19451544, PubMed:19635780, PubMed:21419681, PubMed:21926993, PubMed:23063653, PubMed:24488111, PubMed:36182693). Also functions in miRNA loading and assembly of the Argonaute 1 (AGO1)-containing RNA-induced silencing complex (miRISC), with the miRNAs serving as a guide to direct the miRISC to complementary RNAs to degrade them or prevent their translation (PubMed:15066283, PubMed:17928574, PubMed:19451544). Independently of its catalytic activity, functions in the siRNA silencing pathway by promoting assembly of the siRNA-directed Argonaute 2 (AGO2)-containing RISC (siRISC) (PubMed:15066283). Required for the proper formation of a stable intermediate (R2) in siRISC assembly, which is formed from the R1 precursor complex (containing Dcr-2, R2D2 and the siRNA) and is used for assembly of the mature (R3) siRISC complex (PubMed:15066283). It is not required for siRNA biogenesis (PubMed:15066283, PubMed:21419681). During embryogenesis, involved in germline fate determination (PubMed:16949822).<ref>PMID:11201747</ref> <ref>PMID:11498593</ref> <ref>PMID:15066283</ref> <ref>PMID:15918769</ref> <ref>PMID:15985611</ref> <ref>PMID:16949822</ref> <ref>PMID:17666393</ref> <ref>PMID:17928574</ref> <ref>PMID:19451544</ref> <ref>PMID:19635780</ref> <ref>PMID:21419681</ref> <ref>PMID:21926993</ref> <ref>PMID:23063653</ref> <ref>PMID:24488111</ref> <ref>PMID:36182693</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
-In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner LoqsPB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer1LoqsPB heterodimer. The Dicer-1 dsRBD and three LoqsPB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer1LoqsPB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release.
+In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner LoqsâPB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicerâ1âLoqsâPB heterodimer. The Dicer-1 dsRBD and three LoqsâPB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicerâ1âLoqsâPB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release.
-Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB.,Jouravleva K, Golovenko D, Demo G, Dutcher RC, Hall TMT, Zamore PD, Korostelev AA Mol Cell. 2022 Nov 3;82(21):4049-4063.e6. doi: 10.1016/j.molcel.2022.09.002. Epub, 2022 Sep 30. PMID:36182693<ref>PMID:36182693</ref>
+Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB.,Jouravleva K, Golovenko D, Demo G, Dutcher RC, Hall TMT, Zamore PD, Korostelev AA Mol Cell. 2022 Nov 3;82(21):4049-4063.e6. doi: 10.1016/j.molcel.2022.09.002. Epub , 2022 Sep 30. PMID:36182693<ref>PMID:36182693</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>